On Feb 11, 2015, at 9:32 AM, Roland Fehrenbacher wrote:
>
> Anyone can judge the real impact of this?
>
Other groups have worked on similar capability.
http://bioinformatics.oxfordjournals.org/content/early/2014/02/12/bioinformatics.btu071.abstract
These are essentially data-parallel soluti
Hello Andreas,
Don’t take my opinion as absolute, but I have used bowtie quite a bit in the
past. According to the manual, for that specific example:
Example 5: -a —best
"Specifying -a results in the same alignments being printed as if just -a had
been specified, but they are guaranteed to be
Hello,
On Apr 28, 2014, at 2:32 AM, Andreas Tille wrote:
> [Debian Med list in CC]
> Hi Marc,
>
> On Sun, Apr 27, 2014 at 09:57:23AM +0200, Marc Haber wrote:
>> On Fri, 25 Apr 2014 20:53:01 +0200, Andreas Tille
>> wrote:
>>> Description : efficient mapping of short reads with periodic spac
2012, at 2:21 PM, Andreas Tille wrote:
> Hi Scott,
>
> On Fri, Mar 30, 2012 at 12:37:34PM -0500, Scott Christley wrote:
>> Not sure ITP made it to list...
>
> You can always check the mailing list archive in case you are unsure and
> you would have found it here[1].
>
&g
Not sure ITP made it to list...
Begin forwarded message:
> Resent-From: Scott Christley
> From: Scott Christley
> Date: March 29, 2012 3:47:18 PM CDT
> Resent-To: debian-bugs-d...@lists.debian.org
> To: sub...@bugs.debian.org
> Resent-Cc: debian-med@lists.debian.org, w...@de
Package: wnpp
Severity: wishlist
Owner: Scott Christley
X-Debbugs-CC: debian-med@lists.debian.org
Package name: libkawa
Version : 1.6.1
Upstream Author : Per Bothner
URL : http://www.gnu.org/software/kawa/
License : MIT
Programming Lang: Java
Description
Hello Andreas,
I enabled the java build within Swarm, it appears to compile correctly and now
I'm working on getting the right files in the package. I've discovered that
Swarm uses KAWA [1] and the kawa.jar file is just included with Swarm. My
understanding is that packages cannot just provid
Hi Andreas,
Oh sorry, I thought I posted my results but apparently not! The upgrade was a
no go, everything download and installed okay but upon reboot the machine
froze. If I get a chance then I will try to install the testing distribution.
In the meantime, I've been working with upstream on
Hi Andreas,
I have committed my changes.
On Mar 7, 2012, at 2:39 PM, Andreas Tille wrote:
> So you are working on stable which is fine. Please try
>
> apt-cache policy lintian
>
> It should mention newer versions for testing and unstable. If not
> please adapt your sources.list to also ment
Hello Andreas,
On Mar 6, 2012, at 4:07 PM, Andreas Tille wrote:
> Hi Scott,
>
> On Sat, Mar 03, 2012 at 12:12:38AM +0100, Andreas Tille wrote:
>>> W: libswarm source: debhelper-but-no-misc-depends libswarm2-dev
resolved
>>> W: libswarm source: newer-standards-version 3.9.2 (current is 3.9.1)
y and helps other potential users outside Debian as well
> (which is a good thing). I will keep on helping to finalise the package
> once Luis will confirm success in getting cmake working.
>
>
> An explicite thanks to Luis who made me realise that MoM might be really
>
Hello Andreas,
On Jan 19, 2012, at 3:14 AM, Andreas Tille wrote:
> Hi Scott,
>
> On Wed, Jan 18, 2012 at 04:07:06PM -0600, Scott Christley wrote:
>> I have committed a few changes to the swarm package, most notably the
>> passing of correct parameters to configure, so now
Hello Chris,
Can you tell me the status of this bug? There are patches available which
correct the segmentation fault, and I need this patched version so the software
I'm packaging [1] will work correctly.
thanks
Scott
[1] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=611922
--
To UNSUB
Hello,
I have committed a few changes to the swarm package, most notably the passing
of correct parameters to configure, so now the package looks to build
completely. However, the deb files are essentially empty. Could somebody
please take a look and give me a hint for how to package shared l
0100
> + -- Andreas Tille Thu, 12 Jan 2012 22:18:50 +0100
>
> libswarm (2.3.0-1) unstable; urgency=low
>
>
> Modified: trunk/packages/swarm/trunk/debian/control
> ===
> --- trunk/packages/swarm/trunk/debian/control 2012-01-12 18:52:47 UTC (rev
> 926
biococoa.app is obsolete, and should be removed so as not to confuse with
libbiococoa, where functionality now resides. sequenceconverter.app is old
code but has the chance of being updated by upstream, are there bugs with that
package?
Scott
On Oct 22, 2011, at 11:17 PM, Charles Plessy wrote
On Feb 18, 2011, at 4:13 AM, Andreas Tille wrote:
> On Fri, Feb 18, 2011 at 10:22:40AM +0900, Charles Plessy wrote:
>> there is also the problem that a non-free source package is not allowed to
>> produce binary packages for the main archive… Perhaps the best solution for
>> the
>> moment is to
On Feb 17, 2011, at 7:22 PM, Charles Plessy wrote:
> Le Thu, Feb 17, 2011 at 10:42:26PM +0100, Andreas Tille a écrit :
>> On Thu, Feb 17, 2011 at 07:24:59PM +0100, Steffen Möller wrote:
>>> glam2 has found its way to meme only at some later point as it seems. What
>>> counts are the source tarba
Hello,
I was looking at the meme packaging and noticed that it hadn't been finished,
so I've made a few changes and have gotten it to build. However I have a
question. MEME is actually a suite of programs. In the current packaging,
there is a separate package for one of the programs (glam2).
Hello,
I get the following error when trying to build the biomaj debian package from
SVN. Anybody know what the error is? I'm guessing a missing dependency.
thanks
Scott
compile:
[mkdir] Created
dir:
/home/scottc/Projects/tools/debian-med/trunk/packages/biomaj/build-area/biomaj-1.1.0/usr
Hello,
I have committed the initial packaging for maude into SVN. lintian was clean.
Please review and upload if it looks good!
thanks
Scott
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Archive:
Tille wrote:
> On Thu, Feb 10, 2011 at 03:44:11PM -0600, Scott Christley wrote:
>> I just committed the initial packaging for libtecla, ITP bug #612625. I
>> would be happy if somebody could review my package.
>>
>> When I run lintian I get these messages, I kinda understan
gt; http://neuro.debian.net/pkgs/fsl-feeds.html.
>
> I am not suggesting to replace all those data provider systems created
> by professionals ;) I am talking about complimenting them
> whenever feasible/sensible for the Debian needs/purposes.
>
> On Tue, 15 Feb 2011, Scott Chr
so we need to provide the Jar
> files with the softs.
> The "core" e.g. the main program that is called by the web interface will be
> in free.
>
> Core can also be used without the web interface, but interface is definitly a
> plus
>
> Olivier
>
the community have developped around the tool (available on
> the web site).
> Those propery files would be an add-on package to Biomaj (for the moment we
> have to manually put those in Biomaj bank directory).
>
> Regards
>
> Olivier
>
> Le 2/15/11 9:24 PM, Scot
I think putting the data itself into debian repository is problematic.
Regardless of any licensing issue, the shear amount of data is too great.
Better to let the professionals who are getting paid to manage the data (NCBI,
KEGG, etc.) and download directly from those sites. Pretty much all
Hello,
I wonder if anybody has thought about providing large data sets, like genomes,
microarray data, etc. into debian "packages" in a way that makes it easy for
users to get those data sets onto their machine, making it easier to use
various tools? I can think of many great ways this would b
On Feb 11, 2011, at 8:23 AM, Michael Banck wrote:
> On Wed, Feb 09, 2011 at 10:18:15AM -0600, Scott Christley wrote:
>> Description : Tecla is a command-line editing library
>>
>> The tecla library provides UNIX and LINUX programs with interactive
>> command line
Hello,
I just committed the initial packaging for libtecla, ITP bug #612625. I would
be happy if somebody could review my package.
When I run lintian I get these messages, I kinda understand the errors but am
not sure how to resolve. For example, how do I indicate this package closes an
ITP
Package: wnpp
Severity: wishlist
Owner: Scott Christley
X-Debbugs-CC: debian-med@lists.debian.org
Package name: libgbfp
Version : 0.6.1
Upstream Author : GreenGene BioTech Inc.
URL : http://code.google.com/p/gbfp/
License : GPL
Programming Lang: C
Description
Package: wnpp
Severity: wishlist
Owner: Scott Christley
X-Debbugs-CC: debian-med@lists.debian.org
Package name: libtecla
Version : 1.6.1
Upstream Author : Martin C. Shepherd
URL : http://www.astro.caltech.edu/~mcs/tecla/
License : MIT
Programming Lang: C
I tried adding the X-Debbugs-CC tag in my ITP, but I don't think it worked, the
email I sent is below anybody know what I'm doing wrong?
Scott
Begin forwarded message:
> From: Scott Christley
> Date: February 3, 2011 3:00:56 PM CST
> To: sub...@bugs.debian.org
> Subject
Begin forwarded message:
> From: Scott Christley
> Date: February 3, 2011 1:42:27 PM CST
> To: sub...@bugs.debian.org
> Subject: ITP: libswarm -- Swarm is a framework for agent-based simulation
>
> Package: wnpp
> Severity: wishlist
> Owner: Scott Christley
>
&
On Oct 2, 2010, at 3:55 AM, Charles Plessy wrote:
> Le Thu, Sep 30, 2010 at 08:49:11AM +0200, Andreas Tille a écrit :
>>
>> when browsing through the list of packages which have incomplete
>> information in our tasks files I stumbled uppon SequenceConverter.app.
>> Historically this program once
On Sep 13, 2010, at 4:00 PM, Andreas Tille wrote:
> Scott, you once worked on this package. Would you volunteer to prepare
> final packages for upload. I'm currently a bit distracted by other
> tasks (GNUmed packaging, some Blends infrastraucture things, etc.) For
> sure other volunteers are w
BioCocoa is ready for upload! The bits of code under question were re-released
under the Lucent Public License 1.02 which should pass Debian guidelines.
Sorry it took so long!
cheers
Scott
On Apr 23, 2010, at 1:11 AM, Andreas Tille wrote:
> On Thu, Apr 22, 2010 at 01:40:43PM -0700, Sc
On Apr 24, 2010, at 9:06 PM, Steve M. Robbins wrote:
> On Sat, Apr 24, 2010 at 11:14:31AM -0700, Scott Christley wrote:
>
>> Then when I use the svn-b alias (svn-buildpackage -us -uc -rfakeroot
>> --svn-ignore) the output is this:
>
>> chmod a+x
>> /home
On Apr 23, 2010, at 7:43 PM, Scott Christley wrote:
> Has anybody put together a package that uses the standard GNU autotools to
> configure? Everything I read seems to indicate that the debian/rules file is
> very simple, yet it is not working for me. It complains that th
Hello,
Has anybody put together a package that uses the standard GNU autotools to
configure? Everything I read seems to indicate that the debian/rules file is
very simple, yet it is not working for me. It complains that there is no
configure file. However, there is definitely a configure fil
On Apr 22, 2010, at 2:29 PM, Andreas Tille wrote:
> On Thu, Apr 22, 2010 at 01:50:10PM -0700, Scott Christley wrote:
>> Hi Andreas,
>>
>> I should have a copy of Jakson's files. I was using them to give me hints
>> for packaging Swarm. The upstream Swarm c
.
Is there a date set for the freeze?
Scott
On Apr 22, 2010, at 1:17 PM, Andreas Tille wrote:
> Hi Scott,
>
> On Thu, Oct 08, 2009 at 10:37:59AM -0700, Scott Christley wrote:
>>
>> On Oct 7, 2009, at 10:24 PM, Andreas Tille wrote:
>>
>>> would you mind contacti
Hi Andreas,
I should have a copy of Jakson's files. I was using them to give me hints for
packaging Swarm. The upstream Swarm code has changed significantly so the
packaging needs to be updated. I have the files in my local Debian Med
checkout, so I suppose I should commit them sometime soon
On Oct 7, 2009, at 10:24 PM, Andreas Tille wrote:
would you mind contacting upstream about this issue because you are
obviousely well informed ?
Yes, will do.
Scott
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tream might just want to rewrite those functions.
thanks
Scott
On Oct 7, 2009, at 1:08 PM, Andreas Tille wrote:
On Wed, Oct 07, 2009 at 10:55:20AM -0700, Scott Christley wrote:
Is there any way to check status of upload?
The maintainer gets information about the status. In our case this i
On Sep 21, 2009, at 12:31 AM, Andreas Tille wrote:
On Sun, Sep 20, 2009 at 07:18:02PM -0700, Scott Christley wrote:
A new upstream release of BioCocoa. The package should be completely
covered by a BSD style license, so hopefully all of the license
issues
are resolved now. I've up
Hello all,
A new upstream release of BioCocoa. The package should be completely
covered by a BSD style license, so hopefully all of the license issues
are resolved now. I've updated the packaging files for the new
release. I appreciate if somebody can review my changes.
thanks
Scott
On Fri, Aug 07, 2009 at 09:18:05AM +0200, Mathieu Malaterre wrote:
On Thu, Aug 6, 2009 at 8:57 PM, Scott Christley
wrote:
If somebody would like to work with me to package them, I will
definitely
help.
Count me in ! though I do not know those packages. I just happen to
start working in a diff
I'm definitely interested in Swarm; I'm very familiar with it. It
does have Java but it is mainly Objective-C, the Java part is extra.
I am also familiar with Repast though not as much.
If somebody would like to work with me to package them, I will
definitely help.
cheers
Scott
On Aug 6,
On Mar 25, 2009, at 7:43 AM, Yavor Doganov wrote:
On Wed, Mar 25, 2009 at 07:47:57AM +0100, Andreas Tille wrote:
I'd be very happy if somebody might have a look at biococoa.
Hi Andreas -- there are some serious issues with it.
GNUstep frameworks are packaged like classic shared libraries (t
neral I wonder what the current status of Biococoa.app might be.
Scott Christley has split up a separate application
sequenceconverter.app
but neither a new biococoa.app nor sequenceconverter.app was finally
uploaded.
Scott could you please elaborate on your plans for an upload? Any
blocke
Hey Charles,
I've done GSoC for the Swarm Development Group the last two years.
The first year we got three students, I mentored two of them. Last
year I volunteered to mentor, but we got only two students and my
projects didn't get picked.
We took both approaches, we listed a lot of pr
On Oct 18, 2008, at 7:00 AM, Charles Plessy wrote:
just let us know when updated packages are available. Also, if you
want
to make stronger tests of your biococoa package, you can try to
package
your software for ultraconserved elements, depending on your updated
biococoa package, and test
Hello,
There is a software package called Swarm (http://www.swarm.org) which
is an agent-based simulation toolkit that I would like to package into
Debian. Is debian-med interested in modeling and simulation
software? Systems biology? Or do you think there is another more
appropriate g
Hello Charles,
On Oct 15, 2008, at 5:04 PM, Charles Plessy wrote:
nice work ! Now we have working BioCocoa and SequenceConverter
packages :)
Would you like to add your name in the 'Uploaders:' field of
debian/control and become maintainer of them?
Ok, sure.
I have two other unrelated ques
On Oct 13, 2008, at 1:21 AM, Charles Plessy wrote:
Le Sun, Oct 12, 2008 at 11:40:11PM -0700, Scott Christley a écrit :
The sequence converter code doesn't seem to compile with version 2.X,
so I think it needs to either be rewritten or maybe functionality is
missing from 2.X, I'
On Oct 12, 2008, at 10:54 PM, Charles Plessy wrote:
Le Sun, Oct 12, 2008 at 03:57:33PM -0700, Scott Christley a écrit :
So I got BioCocoa to produce a new source code release, and worked on
modifying the package files. The patch is not very big so I've
attached
it. This is my
Hello,
So I got BioCocoa to produce a new source code release, and worked on
modifying the package files. The patch is not very big so I've
attached it. This is my first attempt, so I welcome any comments.
The resultant deb installs fine, and I compiled some code against the
installed
raded, I will retry.
cheers
Scott
On Sep 27, 2008, at 6:55 PM, Scott Christley wrote:
Okay, ran into my first issue. I checked out the Debian Med svn
repository, got the latest BioCocoa source code put into a tarball,
and am now trying the svn-buildpackage command. It gives me an error:
Okay, ran into my first issue. I checked out the Debian Med svn
repository, got the latest BioCocoa source code put into a tarball,
and am now trying the svn-buildpackage command. It gives me an error:
dpkg-checkbuilddeps: Unmet build dependencies: libgnustep-gui-dev (>=
0.12.0)
Insuff
Greetings,
Thanks to Charles Plessy for directing me to this list.
I am a developer for BioCocoa, which is an GNUstep framework for
bioinformatics, and I would like to have BioCocoa provided as a Debian
package. My understanding is there is an existing package,
biococoa.app, but it is jus
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